Contacts of the helix formed by residues 749 - 763 (chain C) in PDB entry 6CIM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 749 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716C GLU* 5.1 1.8 - - - -
747C THR 3.8 3.3 + - - -
748C ARG* 1.3 76.4 - - - +
750C HIS* 1.3 65.6 + - - +
751C ALA* 3.8 5.7 + - - +
752C GLU* 3.3 23.3 + - - +
753C ASN* 3.0 26.9 + - - -
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Residues in contact with HIS 750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C GLU* 2.5 30.5 + - - +
749C SER* 1.3 74.4 - - - +
751C ALA* 1.3 57.8 + - - +
753C ASN* 3.1 3.9 + - - +
754C LEU* 2.9 58.5 + - + +
783C PRO* 3.4 26.2 - - + +
784C PHE* 3.9 6.0 + - - -
785C ILE 3.3 27.8 + - - -
786C GLU* 3.6 44.8 + - + +
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Residues in contact with ALA 751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749C SER* 3.2 5.6 + - - +
750C HIS* 1.3 77.3 - - - +
752C GLU* 1.3 65.7 + - - +
754C LEU* 3.2 13.3 + - + +
755C GLN* 3.0 24.1 + - - +
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Residues in contact with GLU 752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747C THR* 3.6 20.7 - - - +
748C ARG* 3.3 24.4 - - - +
749C SER* 3.2 19.7 + - - +
751C ALA* 1.3 78.9 - - - +
753C ASN* 1.3 61.3 + - - +
755C GLN* 3.4 7.5 + - - +
756C ARG* 2.9 73.8 + - + +
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Residues in contact with ASN 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C GLU* 3.6 36.5 + - - +
718C LEU* 4.1 8.5 - - - +
728C THR 6.0 0.2 + - - -
748C ARG* 4.0 21.5 + - - +
749C SER 3.0 17.0 + - - +
750C HIS* 3.6 8.3 - - - +
751C ALA 3.1 0.4 - - - -
752C GLU* 1.3 83.7 - - - +
754C LEU* 1.3 59.6 + - - +
756C ARG* 3.3 2.9 + - - -
757C TYR* 2.9 26.7 + - - +
779C VAL* 3.3 28.6 - - + +
783C PRO* 3.6 16.8 - - + -
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Residues in contact with LEU 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750C HIS* 2.9 45.1 + - + +
751C ALA* 3.2 10.7 + - + +
753C ASN* 1.3 75.1 - - - +
755C GLN* 1.3 58.1 + - - +
757C TYR* 3.4 6.8 + - - +
758C GLU* 3.0 24.8 + - - +
782C LYS* 4.3 17.5 - - + +
783C PRO* 3.4 42.6 - - + +
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Residues in contact with GLN 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751C ALA 3.0 15.0 + - - +
752C GLU* 3.9 6.4 - - - +
754C LEU* 1.3 76.3 - - - +
756C ARG* 1.3 63.6 + - - +
758C GLU* 3.2 9.5 + - + +
759C VAL* 2.9 52.2 + - - +
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Residues in contact with ARG 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731C ASP* 2.7 43.8 + - - -
747C THR* 5.4 0.2 - - - +
748C ARG* 4.1 9.3 - - - +
752C GLU* 2.9 55.5 + - + +
753C ASN* 3.3 5.3 + - - +
755C GLN* 1.3 75.3 - - - +
757C TYR* 1.3 66.7 + - - +
759C VAL* 3.3 6.7 + - + -
760C TRP* 3.0 19.8 + - - +
775C ARG 4.5 8.0 + - - +
776C VAL* 3.2 34.3 + - + +
777C LYS* 3.9 18.4 - - - +
779C VAL* 3.8 20.0 - - + -
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Residues in contact with TYR 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753C ASN 2.9 12.9 + - - +
754C LEU 3.6 8.7 - - - +
756C ARG* 1.3 77.1 - - - +
758C GLU* 1.3 65.4 + - + +
760C TRP* 3.2 8.6 + + - +
761C ARG* 2.8 57.6 + - + +
779C VAL* 3.7 9.2 - - + +
780C SER 3.8 15.3 - - - -
781C ALA 3.3 28.0 - - - +
782C LYS* 3.5 42.8 - - + -
783C PRO* 4.0 1.8 - - + -
36D TRP* 3.5 29.1 - + - -
68D TYR 5.1 1.4 + - - -
70D PRO* 3.6 17.3 - - - +
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Residues in contact with GLU 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754C LEU 3.0 14.3 + - - +
755C GLN* 3.2 15.2 + - + +
757C TYR* 1.3 85.0 - - + +
759C VAL* 1.3 57.3 + - - +
761C ARG* 2.6 44.1 + - - -
762C SER* 2.9 36.8 + - - +
782C LYS* 5.8 1.9 + - - -
106D LYS* 5.4 1.5 - - - -
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Residues in contact with VAL 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755C GLN* 2.9 39.0 + - - +
756C ARG* 3.6 11.0 - - + +
757C TYR 3.2 0.2 - - - -
758C GLU* 1.3 74.6 - - - +
760C TRP* 1.3 61.5 + - - +
762C SER* 3.8 5.6 - - - -
763C ASN* 2.9 27.5 + - - -
764C PRO* 3.4 17.5 - - + +
765C TYR* 6.0 2.0 - - + -
772C LEU* 3.9 3.7 - - + +
775C ARG* 3.4 33.7 - - + -
776C VAL* 3.6 11.2 - - + -
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Residues in contact with TRP 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756C ARG 3.0 13.6 + - - +
757C TYR* 3.5 13.0 - + - +
759C VAL* 1.3 78.0 - - - +
761C ARG* 1.3 67.3 + - - +
763C ASN 3.7 2.4 + - - -
769C VAL* 3.9 22.0 - - + -
772C LEU* 3.5 41.3 - - + +
773C ARG* 3.9 29.2 - - + -
776C VAL* 3.9 12.8 - - + -
779C VAL 3.7 9.0 - - - +
780C SER* 3.6 49.4 + - - -
37D PRO* 6.3 0.4 - - - +
39D ARG* 5.9 1.8 - - - -
42D PRO* 4.0 23.0 + - + -
68D TYR* 3.6 45.8 + + + +
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Residues in contact with ARG 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757C TYR* 2.8 44.4 + - + +
758C GLU* 2.6 44.8 + - - +
760C TRP* 1.3 79.6 - - - +
762C SER* 1.3 72.5 + - - +
67D CYS* 3.7 8.8 - - - +
68D TYR 3.2 39.5 + - - +
69D LEU* 5.1 0.7 - - - -
70D PRO* 4.7 4.3 - - + -
106D LYS* 3.2 29.8 - - - +
108D TYR* 3.2 25.9 + - - +
126D GLU* 2.7 39.4 + - - +
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Residues in contact with SER 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758C GLU* 2.9 27.4 + - - +
759C VAL* 3.8 1.0 - - - -
761C ARG* 1.3 92.1 - - - +
763C ASN* 1.3 70.6 + - - +
764C PRO* 3.0 26.8 - - - +
66D SER 4.8 0.3 - - - +
67D CYS* 4.3 14.6 - - - -
126D GLU* 5.0 3.6 - - - -
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Residues in contact with ASN 763 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759C VAL 2.9 13.7 + - - -
760C TRP 3.7 2.4 + - - +
761C ARG 3.5 1.2 - - - -
762C SER* 1.3 75.7 - - - +
764C PRO* 1.3 68.1 - - - +
765C TYR 4.3 0.9 + - - -
766C HIS* 3.2 15.7 + - - +
767C GLU* 3.0 47.6 + - - +
772C LEU* 4.0 21.0 - - + +
63D SER 4.8 0.6 + - - -
64D LYS 3.2 14.8 + - - -
65D ASP 6.0 0.2 - - - -
66D SER 3.1 28.7 + - - +
67D CYS* 4.8 0.4 - - - -
68D TYR* 4.2 10.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il